Westpac Life Saver Rescue Helicopters chief executive Stephan Leahy said a crew was on the scene within minutes, searching for survivors.

Mr Leahy said after a short search a middle-aged man was located and taken ashore, but was unable to be revived.

A search-and-rescue operation for the second person, involving boats and a helicopter, has been stopped for the night and will resume at first light on Monday.

Inspector Angela Burnell says it is a tragic incident.

"We naturally feel for the people who are involved and touched by this," she said.

"It's going to touch our community. It's a small community down here and these kind of events have a big impact."

Moruya Aeroclub pilot and chief flying instructor Sheldon Jones said the plane departed from Moruya Airport on a local flight, believed to be a bi-annual flight review or "check flight", which all licensed pilots must regularly undertake.

Mr Jones said the two men on board were experienced pilots, and both are believed to be locals.

"We can only speculate that something mechanical has happened," he said.

A Westpac Life Saver rescue helicopter, water police, lifesavers and Marine Rescue NSW were involved in the search on Sunday.